VCF files
Hello, I run this code for produce VCF files of samples that i work on it :
java -jar picard.jar MarkDuplicates \
INPUT=/home/zr/SRR3229050/SRR3229050_sorted.bam \
OUTPUT=SRR3229050_sorted.rmdup.bam \
METRICS_FILE=SRR3229050.dedup.Metrics \
VALIDATION_STRINGENCY=LENIENT \
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=50
I want to sure this code is true? And I want to know how can I check that my vcf files that produced are true and valid?
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Kevin Blighe
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Sanazarghami4444 •
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Sanazarghami4444 •
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Please follow the workflow for Germline short variant discovery (SNPs + Indels):
Kevin
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Kevin Blighe
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this code is part of a larger workflow that map the fastq to bam file before calling the VCF. But this code alone is unrelated to the VCF format.